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CMS / Composite of Multiple Signals
A tool for identifying regions that are under positive selection in the genome and for localizing the causal variant within these regions. CMS generates a composite score based on three distinct signatures of selection: long-range haplotypes, differentiated alleles, and high frequency derived alleles. By combining several, nearly-independent signals, CMS detects signals of positive selection at a much higher resolution than conventional tests, often at the level of single genes. It also has better power than haplotype-based methods for finding regions under selection, especially when the selection signal is fairly old (~20-35 kya).
Implements three complementary methods for detecting sites under selection. Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. This web app is linked to a cluster of computers so that analyses which would take a long time to run on a desktop computer can be run quickly. It provides a user-friendly web interface to a wide collection of state-of-the-art statistical techniques for estimating dS and dN and identifying codons and lineages under selection, even in the presence of recombinant sequences.
INSIGHT / Inference of Natural Selection from Interspersed Genomically coHerent elemenTs
Estimates probability of mutational fitness consequences inferred from patterns of genetic variation. INSIGHT contrasts patterns of polymorphism and divergence in a collection of dispersed genomic sites with those in nearby neutrally evolving sites, accounting for negative and positive selection. It integrates evolutionary and functional data in characterizing the potential functional importance of genomic regions.
Allows to detect ancient sweeps based on a signal of extended lineage sorting. ELS-hmm is able to detect ancient events of positive selection and can differentiate those from background selection. It uses a refined version of a hidden Markov model (HMM) that identifies regions in the genome where the Neandertal and Denisovan individuals fall outside of present-day human variation. The tool models explicitly the longer regions produced under selection, and includes the fixed differences between archaic and modern human genomes as an additional source of information.
MKT / McDonald Kreitman Test
Allows performing McDonald Kreitman Tests (MKTs) not only for synonymous and nonsynonymous changes, as the test was initially described, but also for other classes of regions and/or several loci. The website has three different interfaces: (i) the standard MKT, where users can analyze several types of sites in a coding region, (ii) the advanced MKT, where users can compare two closely linked regions in the genome that can be either coding or noncoding, and (iii) the multi-locus MKT, where users can analyze many separate loci in a single multi-locus test.
Hierarchical Boosting
A machine-learning classification framework that exploits the combined ability of some selection tests to uncover different polymorphism features expected under the hard sweep model, while controlling for population-specific demography. As a result, we achieve high sensitivity toward hard selective sweeps while adding insights about their completeness (whether a selected variant is fixed or not) and age of onset. Hierarchical Boosting also determines the relevance of the individual methods implemented so far to detect positive selection under specific selective scenarios.
SpectralTDF / Spectral representation of Transition Density Functions
Computes the transition density function (TDF) of the diffusion approximation of the Wright-Fisher process with general diploid selection and recurrent mutation. SpectralTDF program allows for populations with selection, mutation, and demographic parameters that vary over time in a piecewise constant manner. It provides a flexible and efficient tool for studying the evolution of allele frequencies over time under complex evolutionary scenarios.
A population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual loci. PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. PopGenome is linked to Hudson's MS and Ewing's MSMS programs to assess statistical significance based on coalescent simulations. PopGenome's integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics.
S/HIC / Soft/Hard Inference through Classification
Allows users to locate sweeps. S/HIC is an approach based on an extremely randomized trees classifier coupled to a supervised machine learning classification technique. It can make distinction between hard and soft sweeps, regions linked to sweeps and those which are neutral. It can be applied for decreasing searches for a target locus of selection by determining more accurate candidate regions. However, it only can be used with phased genotype data.
Facilitates genome-wide scans of selection based on the analysis of long-range haplotypes. Rehh is an R package that detects the footprints of recent or ongoing selection with several graphical functions that help visual interpretation of the results. This method uses extended haplotype homozygosity (EHH)-related statistics. It also includes computation of integrated haplotype score (iHS) (within population) and the cross-population EHH (XP-EHH) (across pairs of populations) statistics.
Clear / Composition of Likelihoods for Evolve And Resequence Experiments
Finds regions and variants under selection evolve-and-resequence (E&R) experiments. Clear can determine populations size and tests hypotheses. It does not compute exact likelihood of a region. This tool adjusts for heterogeneous coverage of pool-seq data and exploits the presence of linkage within a region to compute a composite likelihood ratio statistic. The statistic returned by the tool can be adjusted for other scenarios, including changing population sizes when the demography is known.
PSP / Prokaryotic Selection Pressure
Allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily. PSP is an open access web server, which is designated for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KEGG Orthology (KO), Gene Ontology (GO) or Clusters of Orthologous Groups (COG) terms.
POTION / POsitive selecTION
Allows users to construct and check hypotheses regarding the occurrence of site-based evidence of positive selection in non-curated, genome-scale data within a feasible time frame. POTION is an open source, modular and end-to-end software for genome-scale detection of positive Darwinian selection in groups of homologous coding sequences. It reduces false positives through several sophisticated sequence and group filters based on numeric, phylogenetic, quality and conservation criteria to remove spurious data and through multiple hypothesis corrections, and considerably reduces computation time thanks to a parallelized design.
JCoDA / Java Codon Delimited Alignment
Performs evolutionary analysis on homologous coding sequences. JCoDA is a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. It can be used to rapidly screen for genes and regions of genes under selection using PAML. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs.
IDEA / Interactive Display for Evolutionary Analyses
Provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. IDEA is an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time.
Provides a simple R-based interface into which the user can upload the required data (polymorphism and divergence data for the genomic test region and a neutrally evolving reference region). asymptoticMK is a web-based tool for executing the asymptotic McDonald–Kreitman test. The web service analyzes the data and provides plots of the test results. Upon submission of the web form, asymptoticMK conducts its analysis and then opens a results page in a new browser tab, presenting a summary of the input data and the results from the analysis.
iSAFE / integrated Selection of Allele Favored by Evolution
Pinpoints the favored mutation with population genetics signals and boosting approach. iSAFE is a method that exploits coalescent based signals to rank all mutations within a 5Mbp around a region under selection. This resource was designed to work in regimes where the selection strength is high. It considers only biallelic sites and its performance remains robust to a range of simulation parameters, including a wide range of initial frequencies.
ODoSE / Ortholog Direction of Selection Engine
Allows the calculation of a novel extension of the McDonald-Kreitman (MK) test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome. ODoSE web service uses a graphical user interface (GUI) that enables researchers to select prokaryote genomes of interest from the NCBI database and/or upload their own genome data, after which the DoS statistic is calculated for every individual singlecopy ortholog (SICO). ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization.
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